Shinobi of the Cosmic Era
by neostardustdragon101
Summary: After living for countless centuries Naruto Uzumaki has once again been called into the line of battle. Driven to protect his precious new friend's and family Naruto will wage war alongside his fearsome Monbile Suit Gundam: Kurama. Naruto x Harem
1. Chapter 1

Disclaimer: I do not own either the Naruto and Gundam Seed franchise.

Chapter 1

A young man was busy at work on his laptop, he appeared to around seventeen years old, he had spiked blond hair and cerulean blue eyes, but his most noticeable trait were the six whisker like birth marks on his cheeks. This young man was Naruto Uzumaki, the legendary Savior of the world, Child if prophecy, the Jinchuriki of the Nine Tailed Beast's and most well know the Number One Hyperactive Knucklehead Ninja. After defeating sealing away Kaguya Naruto had been given the sprites of the Nine Biju. After words his life began to change for the better the people who once hated him now admired and respected him for everything he had done, his name had become well known and many people would come to Konoha just to meet him. The five Shinobi Nations were now joined in peace.

Naruto's greatest joy was when he finally achieved his greatest dream one that even was above being the Hokage. He had a family, Naruto had married Hinata Hyuga and have two beautiful children Boruto and Himawari and he eventually achieved his dream of becoming the Seventh Hokage.

However all that was in the past, Naruto served as Hokage for many years years and rose to be recognized as a Hokage with few equal, to the other Hokage before him, while there had been conflict between different ninja lands there had been peace and prosperity as well as cooperation and unity in the land. Despite reaching the age of fifty nine, Naruto still retained his young healthy look and vitality. Naruto had discovered this was a result of his new found powers, eventually Naruto resigned as Hokage to live out his life with Hinata who had told Naruto he should rid himself of her and find someone younger and beautiful instead of a hag like her, but he refused and told her she would always be his beautiful Hime(Princess) no matter what. His clan had grown, he had a large number of children, and grand children, and was now one of the most recognized clans in the rebuilt village of Konoha, something that sent in a good measure of pride in Naruto. After Hinata passed he travels the world just as his master had before him keeping the peace between the nations.

Naruto watched as the world progressed throught the shadows of countless centuries and millennia.

Year 70 of the Cosmic Era, a war rages, on one side is the Earth Alliance, and on the opposite is the space colonies that form ZAFT (Zodiac Alliance of Freedom Treaty). Mankind is divided over human genetic engineering, with normal humans known as 'Naturals' and the genetically altered humans known as 'Coordinators.'

(Cosmic Era)

Naruto was living his life out in the Orb Neutral Colony of Heliopolis, but despite that even he knew that the peace in the colony would not last forever.

" **So Naruto how's your little Project coming**?" Kurama asked in his small kitsune form hopping atop Naruto's shoulder.

Naruto smiled at his life long friend and partner. "It's coming along perfectly." A serious expression crossed the boys face. "I have a strong feeling that the ignorant and blissful peace we've been living is finally about to end. So its best t be prepared." Naruto said looking up at the large figure covered by the shadows. "Isn't that right partner."

...

"Hey Naruto!" The young blond turned to see his friend's Kira Yamato, Tolle Koenig and Miriallia Haw walking towards him.

"Hi," Naruto said smiling at his friends as they walked over to them high fiving Kira and Tolle. "What are you guys up too?"

"Nothing much just heading over to class, what about you?" Kira asked.

"Just going to finishing with my little project." Naruto replied.

"Any chance you'll finally tell us about it?" Tolle asked putting his arm around Naruto's shoulder

Naruto simply chuckled. "Nope, sorry but your just gonna have to wait and see dude." Naruto said before walking off

(Meanwhile in Space.)

"And there you have it," Replied the captain of the EA transport ship as it docked with the colony. "This old girl has just completed her final mission." He turned to the man next to him. "You served admirably as an escort, Lieutenant La Flaga. I am in your debt."

"Sir," Lieutenant La Flaga said as he turned to face the captain. "I'm just glad we arrived without incident." As if thinking of something, he asked, "Any ZAFT vessels in the vicinity?"

"We've spotted two, but it's no cause for alarm," The captain said. "They know they can't initiate any hostile action once we're docked."

"Because it's neutral territory? What a joke, that is." Mu asked with a light chuckle

"Well, it's thanks to them that our plans have progressed this far."The Captain said. "We're fortunate earth has recognized Orb as a nation."

"Excuse us, captain!" A pilot called out, before the old captain turned to acknowledge the pilots in one group. As they saluted each other the pilots left the bridge.

"Think they can handle themselves alone on the ground?" La Flaga asked.

"I know they're young, but they're all top guns who were selected to be G-Pilots. They'll be just fine." The Capitan replied. "However, someone like you would stick out like a sore thumb." Mu had to laugh off the jab at his inability to pilot a Mobile Suit, before he turned around to look out the bridge's view port, suddenly a strange pulse went through him.

In the bridge of the Nazca-class Vesalius, a masked white uniformed man floated to the tactical table and said to his black uniformed compatriot, "Try not to look so frustrated, Ades."

"Well, I doubt it'd be too late if we waited for a reply from the Council, at least…" Frederik Ades began.

"It will be too late," the white coated man said,

"Perhaps… but we risk making Orb our enemy by doing this," Ades remarked.

"It is really not in their policy to make war with other nations, Ades," the Commander said.

Ades simply looked forward, really wishing he had his superior's confidence on the matter…

(Back in Heliopolis)

Naruto was about to enter his apartment building when he suddenly heard a large explison.

"What the hell!" Naruto said narrowing his eyes before they widen to see a ZAFT Mobile Suit nearby.

"Kage Bushin No Jutsu!" Naruto shouted creating several Clones of himself having them transforms into random people. "Alright go out and evacuate as many civilians as possible!"

"Hai!" The clones said before the vanished scattering across the colony.

"Chomei!" Naruto called out summoning a small Seven Tailed Beetle. "I have job for ya buddy."

"Just leave it to good old lucky seven Chomei." The Insect Biju said with a salute.

xxx

Naruto was sitting within a cockpit checking out all the control systems and smirked to see everything was up and running perfectly. "Weapons systems clears, all control systems synch rate 100%, all systems green." Naruto said checking over the control system of the Mobil Suit

U.N-09focusam Kurama

Naruto closed his eyes s he channelled his chakra through out his Mobil Suit, several cables attached themselves to Naruto's back and spined causing the boys eyes to shoot open and Gundam's eyes flashed as it activates. "Alright! Let's Gundam!" Naruto said with a feral grin as his Gundam got on all fours similar to how Naruto would in his tailed beast mode before it smashed though the doors charging through the City like a wild beast.

Naruto closed his eyes and began to focus on his friends trying to find where they were.

Kira was currently inside one of the Earth Forces new G-weapons known as the Strike Gundam. Beside him, lieutenant Murrue Ramius, A beautiful woman, in her twenties with long silky brown hair, perfect skin, beautiful brownish eyes, and very big chest and very beautiful woman. Currently two were surrounded by a group of 4 Ginns.

Kira was had managed to narrowly avoid they're assault but knew he couldn't do it forever.

Naruto's eyes opened and turned to the direction of the Morgenrate facility.

'Not good Kira's a pacifist right to the core, he won't last long." Naruto shot his chakra into his Mobil Shit and charged forward.

The Strike soon found itself blindsided from one of the 4 Ginn's slamming it into a nearby building pinning it down before aiming its rifle at the cockpit.

"Time for you to die you worthless Natural." A Zaft Soldier said with a smirk.

"GET AWAY FROM HIM!" Naruto roared charging forwards slamming his elbow into the head of a nearby Ginn knocking it to the ground.

"What the hell!" The Zaft Pilot shouted.

Kira and Murrue were in shock at the sight of the Mobil Suit, it was slime in form with orange and black coloring its arms and legs were equipped claw like hands and feet.

"Kira, you alright." Naruto called out to his friend causing Kira's eyes to widen.

"N...Naruto!?" Kira exclaimed in shock seeing his friend was piloting a Mobil Suite.

Naruto rubbed his noise with a smirk on his face. "Yeah its me. What do ya think of little project?" Naruto asked

"Project... Wait you built that Mobile Suite!" Kira said shocked to see what his friend had been working on all this time as was Murrue especially. It didn't seem possible that someone so young was capable of creating they're own Mobile Suit.

"Why you miserable bastard!" One of the Zaft Pilots shouted with drawing his sword charging at Naruto. The Kurama drew his sword and charged forward before it vanished in an orange flash.

"Whaa...gack!" The Zaft pilot shouted before he coughed up a huge glob of blood before his Mobil Suit burst into flames with Naruto's Gundam standing over it.

"Now way Christopher! You bastard!" The second Zaft pilot shouted in anger firing his bullets towards the Kurama who held up its arm generating a shield of energy intercepting the bullets.

 **"What the hell**!" Kurama charged forward drawing its beam saber slicing off the Ginns arm picking up its rifle and flooding the cockpit with a barrage of bullets.

"That things a monster!" A pilot shouted aiming its missiles and fired them towards Naruto who effortlessly doged them before slicing the Ginn's legs clean off. He then pulled out 4 Kunai knives and threw them into the last Ginn causing it to exploded.

Nearby an orange Ginn was hovering through the Colony before noticing all four the Ginns sent to retrieve the last Mobile Suite had all been lost. "I've lost the signals from Shawn, Christopher, Thomas and Shu's machines. What the hell is going on." Miguel wondered before he noticed they're was another machine beside the Strike. "What they're was another one we didn't know about." Miguel thought looking over the Kurama and smirked

"Naruto we've got incoming." Kurama said causing Naruto to look up at the Orange Ginn and smirk.

'At least someone besides me knows how badass orange is.' Both Naruto and Miguel thought.

Miguel landed on the ground and mounted his Machine Gun on the GINN's back skirt and brings out its Heavy Sword. Naruto tossed his Machine Gun Aside as well before drawing his own beam saber before the two machines charged at one another with they're machines as they're swords clashed causing sparks to clash between the two blades.

"Kira I want you to get Tolle Miriallia and the others out of here." Naruto shouted over to his friends.

"But what about you?" Kira called out.

"I'll be fine dude just go!" Naruto said with a reassuring reluctantly nodded and followed his friends orders. Naruto smiled seeing his friend's were safely out of the way. "OKAY! Let's do this!" He activated the thrusters and pushed the Ginn back skidding across the ground Miguel punched the Gundam's head knocking it back before driving its knee into Naruto's machines chest bringing down its sword only to be blocked by Kurama's beam saber.

"Not bad..." Miguel said with a smirk pulling back and firing its bullets at Kurama who blocked the all with it's shield before picking up the fallen Ginn's machine gun firing at Miguel who took cover behind a fallen building.

As soon as both guns were out of bullets the two suits charged at each other drawing they're swords as they clashed again.

'Damn it this guys got some good moves.' Miguel thought gritting his teeth.

"Miguel!" Both pilots looked up to see a crimson red mobile armor shaped in thew form of a claw flying towards them unleashing its impulse cannon at the Kurama who swiftly doges attacks before transforming into it's mobile suite mode arming the beam sabers on its wrists as it swiped at Naruto who countered with his own before the Ageis fired at him with its beam rifle.

"We have orders to retreat let's go." Athrun said to Miguel who grudgingly nodded as the two mobile suits took off.

"Looks like they retreating...for now." Naruto said before turning over to the Kurama landed on the ground, Naruto got out of his seat.

"Naruto,Naruto-san!"Naruto turn around to see his friends Tolle, Miriallia, Kuzzy and Sai running towards him.

"Naruto!" Milly shouted as she through her hands around him.

"Hey calm down Mir, you know it takes a lot more than that to kill me." Naruto said patting the girls back.

(Meanwhile)

With both Moebiuses, two of the GINNs and the Marseille III class destroyed, only Mu La Flaga and the other GINN remained.

"Damn it, we need more help!" the Hawk said, firing the Moebius Zero's gun barrels. The attack managed to destroy not only the GINN's assault rifle, but also the entire right arm.

The ZAFT pilot knew he wouldn't last any longer, and wisely decided to withdraw.

Murrue manages to wake up after falling unconscious from blood loss. Kira, Sai, Tolle, and Kuzzey were investigating the Strike and Kurama while Miriallia next to Murrue's awakening form.

The Strike knelt down form to shelter Murrue who was lying underneath. The Kurama was right next to it also in a knelt down form.

With a pained moan, Murrue managed to open her eyes and greeted to the sight of Miriallia and Serena both returned her look with a cheerful smile on their faces.

"I see you're awake." Miriallia says before she looks towards Kira to call him over, "Kira!"

As Kira walks towards her, Murrue holds her head in pain.

"Oh, you'd better stay still for now." He assures her. They both share a silent look as Kira looks guiltily at the ground.

"I'm sorry," he apologises, "I kinda got carried away during that fight and didn't focus on escaping." Miriallia quickly returned after walking away for a few moments with a canteen in Miriallia's hand.

"Care for some water?" She asked Murrue as she gestured the canteen towards her.

"This is awesome, the so-called Gundam!" Tolle said looking over the Kurama.

"You bet it is." Naruto said laughing proud of his creation.

"So this was you special project." Sai said in amazement still not believing Naruto had built this Mobile Suit by himself.

This statement alerts Murrue as she ceases her drinking and looks towards Kira's friends who are investigating the Strike.

"Does it move, or doesn't it?"

"Guy's stop playing with it!" Sai yells up to Toelle and Kuzzey who were currently interacting with the cockpit. Tolle quickly clambered back out.

"Get away from those machines!" Murrue yells out at them. They all turn towards her and are shocked when a bullet clangs next to them on the Strike's chest, causing them to duck their heads in fear.

"Stop! What are you doing?" shouted Kira. "They helped get you out of the cockpit and tended to your wound."

"I am grateful for your help," the Lieutenant said. "But these two machines are part of a top-secret military project. It isn't something civilians should be allowed to touch carelessly."

Deciding it was best not to cause a scene right now Naruto listens to her command and hesitantly steps away from his Kurama

"Stand over there." She commands. They don't hesitate in the slightest and immediately walk over to stand next to the others.

"Tell me your names."

"Sai Argyle."

"Kuzzey Buskirk."

"Tolle Koenig."

"Miriallia Haw."

"Naruto Uzumaki."

"Kira Yamato."

"I'm Murrue Ramius." She declares, "An officer with the Earth Forces."

"I hate to say this, but I cannot allow you to leave." She also declares

"What?" Everyone but Naruto Yells.

"Regardless of how it happened, you have still seen a military secret." Murrue explains to them, "Until I reach the proper authorities and it is determined how the situation shall be handled, you have no choice but to remain here with me at all times."

"You're kidding!" Sai complains.

"You gotta be kidding me." Tolle added, "Are you outta your mind, that's ridiculous."

"Yeah why do we have to stay here while a war is going on!" Miriallia threw into the mix.

"You will do as I say!" Murrue asserts.

"We're citizens of Heliopolis, we're neutral!" Sai exclaims, "We have nothing to do with the military!"

"He's right!" Kuzzey concurs, "besides, what are the Earth Forces even doing here on Heliopolis in the first place? That doesn't make sense in the first place!"

"This is Orb territory we don't have to follow Earth Forces Soldiers!" Miriallia declares.

"That's right!" Tolle agrees.

Their outbursts were silenced as Murrue let off a couple of Pistol shots into the air. She then aims her pistol back on the group of friends.

"Be quiet!" She demands, "you kids do not understand anything!"

"By declaring neutrality and saying you have nothing to do with this, you can distance yourself from the issue." She rehearses, "You don't seriously believe that, do you?"

"The Earth's most vital secret was here and you have seen it." She states, "that is the reality you face."

"That was pretty rough." Sai complains.

"It may be pretty rough" Murrue responds, "But we're at war. Between Earth and The PLANTS. Between Coordinators and Naturals."

Naruto's eyes narrowed at how she used those two words Coordinators, Naturals no matter what they were still just human beings. But some people didn't see it that way to them Coordinators were just freaks against nature. And for what just because they're genes had been alternated that was one thing Naruto hated most as it reminded him of how he was once treated long ago.

(With Rau and Mu)

Rau is hiding behind some cover as he has spotted the enemy Mobile Armor slowly making its way inside Heliopolis. Mu can sense that there is some kind of familiar presence very close to him and instantly notices it when Rau's CGUE dives out of its hiding place and fires a few shots at his Mobile Armor. Mu quickly boosts forward to dodge the oncoming shots.

"Bastard!" Mu yells, "is that you, Rau Le Creuset?!"

He quickly deploys his Gunbarrels to attempt an assault on the CGUE. However, Rau easily dodges the attacks, continuing to fire on the insignificant Mobile Armor.

"You're always getting in my way, Mu La Flaga!" Rau responds, "though we probably share the same opinion!"

He ceases his fire at the Mobile Armor and quickly turns and flies into the entrance into Heliopolis. Mu lets out a growl of frustration as he reconnects his Gunbarrels.

"He's gone into Heliopolis!"

With no time to waste, Mu ignites his boosters and gives chase.

(Back with Naruto Kira and they're Friends.)

X105 Strike here, Earth Forces, please respond!" Kira continues to call over the Radio Headset, desperately hoping that someone would reply, "Earth Forces, please respond!" His only reply was static, he responds to it with a solemn look.

The sound of a large supply truck then alert him as he gets out of the Mobile Suit to see Sai arrive with the vehicle that Murrue had sent him after. Miriallia had decided to stay behind and watch Murrue. Sai quickly disembarks the vehicle and runs up to the group's position.

"The Number five trailer you asked for," He turned around to look back at the Vehicle, which Tolle and Kuzzey were stood next to, clearly exhausted "that's the one right?"

"Yes, thank you." Murrue responds.

"Not bad, I'm guessing the Strike was built with interchangeable armor" Naruto said looking over the Launcher

"Yes but i cannot elaborate any further." Murrue said with a serious face.

"I can respect that" Naruto said holding up his hands defensively.

"Now Kira i want you to go to attach the Launcher pack." Murrue instructed.

Kira nodded and moved the mobile suit over to the truck

Rau just flew out of cover and opened fire on the Moebius Zero. The Mobile Armor is able to dodge the oncoming bursts of fire from the CGUE. Mu lets out a groan of frustration.

"Why, in a place like this?!" He exclaims as he begins to fire shots of his Linear Gun, the yellow beam missing the White Mobile Suit as it strafes to the right and instead colliding with the hangar doors behind it, causing them to explode. Mu flies straight through it and is unfortunately greeted with more burst of Machine Gun fire from the CGUE as it flies backwards. Mu, once again dodges the shots and attempts to acquire a lock. The CGUE flies behind even more cover. Mu lets out a grunt of frustration at this.

"I'd be glad if you disappeared right about now, Mu!" Rau says as he boosts out of his hiding space and manages to land a direct hit on the Moebius Zero's top Gun barrel, causing Mu to deploy them all and eject the damage one, it causes a chain reaction. He retreats in an opposite direction as Rau follows.

On the Archangel

"Launch the ship?" Nuemann asks incredulously, "that's impossible with the number of people we have!" He tries to reason.

"If you time to argue, spend it on finding a way to do it!" Natarle rebuts him, she learns forward with a stern expression, "Morgenroete could still be under attack, you know!"

The door opens and the three Alliance Soldiers known as Jackie Tonomura, Romero Pal and Dalida Lolaha Chandra II as Natarle continues her speech.

"Are you suggesting we remain here and ignore what is happening there?"

"I brought them!" Jackie chirps up, alerting Natarle to their presence.

"Take your seat!" She commands, as she looks back to them, "Just do as the computer instructs you!"

"Yes ma'am!" They all reply as Romero and Dalida enter the two back-to-back seats behind her while Jackie goes to sit in the Co-Pilot's chair.

"Those ZAFT Vessels are still out there!" Nuemann contines to argue, "we're in no position to fight!"

"I know that!" She responds, turning to him, "Prepare to fire Assault Cannons as we activate the ship!"

"You can do that, can't you, Chief Petty Officer?"

He looks at her for a moment before sitting in the pilot's chair and turns back around to face the front.

"Begin takeoff sequence!" She commands, "due to the urgency, we'll omit C-30 to L-21 from the process!"

"Main power, online!"

A countdown timer for takeoff starts for the Archangel as several status readings also appear on the screen.

"Output increase stable." Jackie declares, "450 seconds to required rating."

"That's too long!" Natarle replies, "what's the status of the conduits to Heliopolis?"

"They're unharmed!" Jackie lets out a gasp of surprise.

"Draw power from them!" Natarle continues to order, "Conduit online! Relay power to accumulator!"

"Confirming connection! Flow stable, twenty seconds to required rating!" The timer changed from 450 seconds to 20 seconds. The crew continued going through all systems.

"Life Support Systems satisfactory."

"CIC online"

"Weapon systems online. FCS contact."

"Magnetic field chamber and pellet dispenser idling stable."

"Holding external shock dampener at maximum output."

"Contact main power. Engine stable."

"All Archangel systems online. Preparations for takeoff complete!"

"Seal all airtight bulkheads!" Natarle orders, "All hands, be prepared for sudden impacts and damage to the ship."

"Proceed slowly. Archangel, take off!"

The ship's engines roar into life as the White and Red Battleship slowly starts to move forward through the Debris-ridden hangar. The Archangel's Launch bay doors open as the Lohengrin are brought out and begins charging.

Rau and Mu…

Rau continues to evade to evade Mu's attempt at hitting the CGUE as he dodges every shot from the Moebius Zero's Gun barrels and Linear Gun. He's quick enough to be able to approach the remaining Gunbarrel and crush it with his CGUE'S feet leaving Mu's only weapon being the single Linear Gun mounted on the Moebius Zero. Mu fires a couple of shots with his Linear Gun which are still unable to hit his target.

With The Kurama And Strike

Kira quickly maneuver's the Strike in front of the Supply truck with its back towards it while Naruto inside Kurama going through a simulation battle to improve him piloting skills. The top of the trailer pulls open to reveal its content inside. A standard Power pack which appeared to mount on the back. A green shoulder pad comprised of a 120MM Anti-Ship Gun which looked like a Gatling Gun as well as two 350 MM Gun Launchers. Finally, the "Agni" 320 MM Hyper Impulse Beam Cannon. Kira climbed out of the cockpit of the Strike.

"Which is the power pack?" He queries Murrue loudly so that she can hear him.

"The Weapons and Power Pack are together in one unit!" She explains, "Mount the whole unit!"

Outside the Colony Mu is still desperately trying to evade the CGUE.

"The evacuation orders are still in effect, I guess." Miriallia randomly says.

"I wonder if my father and the others evacuated safely." Sai wonders. Kuzzey lets out a long sigh.

"I wanna hurry up and go home!" He whines.

Naruto walked up to his friend gently patting his shoulders before smacking upside the head.

"Ow!" Kuzzy said with anime tears running own his face nursing a large lump.

"Man up Kuzzy! At this rate your homes probably been destroyed, we've gotta focus on the task at hand." Naruto said glaring at the young man beside him.

"Damn Naruto sure can be harsh at times." Tolle whispered over to Sai who nodded as Naruto helped Kuzzy up.

"Look Kuzzy, things are gonna change from here on out we can't afford to just sit around and complain about everything." Naruto putting a gentle hand on his friends shoulder. "Listen man we need you to be strong."

Kuzzy was still abit scared but quickly swallowed it and nodded the sound of an explosion echoed through the Colony as they looked up to see another Mobile Suite enter Heliopolis.

Everyone looked up to see a ball of fire coming from a part of the central shaft of Heliopolis. A ZAFT Cgue emerged from the fireball, followed by an Earth Forces Moebius Zero. The Cgues Signal eye looks towards where the Strike and Kurama were.

"So those are the two?" He thinks out loud.

"The last unit" Mu also wonders he soon noticed the Kurama and became confused knowing there only 5 new machines.

Rau changes the direction of his CGUE and instead heads straight for the two Gundams. He gets very close before dodges as Mu's Zero heads straight for him. He still kicks up dust as the wind causes Kira's friends to hold their hands up to block it.

"Kurama!" Naruto shouted as his Mobile Suite instantly activated opening it's Cockpit allowing Naruto to jump in. "Alright let's go!" Naruto said as the thrusters activated taking off into the air drawing his beam rifle at the Cgue.

"Well, well in would appear that we missed one. I doesn't matter I'll takle you down now while I have the chance." Rau said confidently as he fired at the Kurama. Kurama flew away from where Kira and the others were. He had to distract the ZAFT machine long enough for the Launcher Striker to be mounted on the Strike Sure enough, the Cgue began to fire as Naruto dodged his energy shots effortlessly.

"Impressive." Rau said with a smirk "But let's see how you fair against a sword," he said over an open frequency as he switched from the CGUE's rifle to its sword.

Naruto smirked at Le Creuset's challenge to him as he pulled out his beam saber.

The Cgue's and the Gundam's swords clashed together, Naruto then separated from the clash and spun Kurama's other arms shield extended into long sword aiming the swing for the Cgue's blocked the attack before using his thrusters and pushed the Kurama back a bit before slashing down on to the Kurama's Shoulder. But the Kurama spun again and dodged the attack while pulling out a Beam Saber with its other hand.

The two machines continued to clash against each other both managing to evade the others blows but then suddenly something exploded in the distance and out came a ship.

"The Archangel…" Murrue breathed as the warship flew into the colony's interior. For a moment, everything seemed to stand still… and then, suddenly, everything got going again, as the Cgue opened fire on the Archangel and the assault ship returned fire with missiles. Unfortunately, the Cgue agilely evaded the missiles, destroying a few, before leading the others to crash into the Central Shaft of the colony.

"Damn you!" Naruto roared ready to charge at him when he heard Kira call out to him.

"Naruto move!" Kira shouted to his friend.

Naruto looked down to see the Strike with its Launcher Pack equipped. Naruto nodded. "He's all yours man take him out."

Gripping the long rifle of the Launcher Striker pack, Kira brought up the targeting computer, forgetting to check the power levels of the weapon. He locked in on the Cgue, and pulled the stared, frozen in horror, as the massive beam of energy lanced out and blasted away the Cgues arm, before proceeding on to blow a whole in the side of the colony.

"What the hell! Whaty kind of power is that!?" Naruto and Kira said in shock witnessing the destruction caused by a single shot from the Gundam.

"We need to head to the Archangel immediately." Murrue said to the kids

(With Le Creuset.)

"How is that possible?" Rau Le Creuset questioned himself as he pulled his CGUE back towards the hole blown in the colony. "A mobile suit with that much firepower…?" A small smile graced the masked man's lips.

The two gundams flew over to the new battleship Kira carried Murrue, Tolle, and the others to the Archangel's open starboard catapult. Stepping into the catapult, Strike knelt down and let the group off of the mobile suit's hand with the Kurama landing beside him as a group of Earth Forces soldiers ran up to them.


	2. Chapter 2

**Hey everyone sorry for the wait but here's the second chapter for Shinobi of the Cosmic Era.**

 **.**

 **.**

Chapter 2

(With Naruto and Kira.)

The two gundams flew over to the new battleship Kira carried Lacus, Murrue, Tolle, and the others to the Archangel's open starboard catapult. Stepping into the catapult, Strike knelt down and let the group off of the mobile suit's hand with the Kurama landing beside him as a group of Earth Forces soldiers ran up to them.

"Lieutenant Ramius!" called a black haired woman at the front of the group, her voice sounding relieved. Murrue looked over at her.

"Ensign Natarle Badgiruel," said Murrue, sounding somewhat relieved herself.

"It's a tremendous relief to see that you're safe," said Natarle as she saluted. Murrue returned the salute.

"You as well," said Murrue. "I'm pleased that you protected the Archangel. You do realize you saved us."

Kira and Naruto opened the cockpitz of the Strike and Kurama and clambered out, drawing shocked stares from the Earth Forces soldiers as he descended from the mobile suit.

"Come on, will someone tell me what's going on here?" asked Murdoch, the Archangel's chief mechanic. "He's just a kid. Just learned how to shave, and he's piloting that thing?"

"What about the other one?"

"Yeah but what about the other one? i didn't know we had a 6th machine." s

"Wait yeah, and look it's still on. it's not loosing it's color."

"Lieutenant Ramius, what's going on?" asked Natarle, her confusion obvious. Murrue glanced over at Kira and Lacus before looking down.

"Wow," came a new voice, drawing everyone's eyes to a blond man in a purple and gray pilot suit walking over to them. "What a surprise," he said as he continued walking up to them.

"I'm Lieutenant Mu La Flaga, of the Seventh Orbital Fleet, at your service" he introduced, stopping in front of Murrue. He then saluted her. "It's an honor." The other soldiers, including Murrue and Natarle, saluted as well.

"Lieutenant Murrue Ramius, of Sector Two, Fifth Special Division," said Murrue, introducing herself as well. "I'm a crewmember of this ship."

"Ensign Natarle Badgiruel, same division," introduced Natarle.

As the soldiers relaxed again, Mu spoke up. "I would like permission to come aboard this vessel," he said. "May I ask who's in command around here?"

Natarle frowned slightly, her expression somewhat downcast. "The captain," she began. "And all of the superior officers of this ship have perished in battle. Therefore, I believe it's Lieutenant Ramius who's next in command."

"Huh?" said Murrue, sounding distinctly worried.

"Only about a dozen of us are left, sir, mostly non-commissioned officers," said Natarle. "Fortunately, I was in the shaft and managed to survive."

"You mean the captain's…? It can't be," said Murrue.

"Oh man, what an unmitigated disaster," said Mu. "In any case, please grant me permission, Lieutenant Ramius. The ship I was assigned to engaged the enemy, and was downed."

"Oh, um, sure, permission granted," said Murrue, obviously uncomfortable with being in command.

"And…" said Mu, turning to look at Naruto and Kira. "And who are they..."

"As you can,see theyI saw him in the factory district during the attack. While fleeing we came across the Strike He successfully used it to disable a ZAFT Ginn." Murrue said shocking crew at this.

"Fight off a Ginn a,that kid actually did it?" Natarle, asked incredulous.

"Yes," Murrue said. "But after we defeated it, we were ambushed and surrounded by 4 more gins, and almost lost our lives if it wasn't for him" she said pointing to Naruto who was leaning against Kurama talking amongst his friends.

"And what about that machine, it wasn't listed amongst the G-weapons." Natarle asked looking over the Kurama.

"From what I've learned recently he built the Mobile Suite himself." Murrue said shocking the crew.

"Are you serious!? A kid built a Mobile Suite by himself that's impossible!" Natarle exclaimed in shock.

"Sorry but that's classified." Naruto said causing the two women to jump in shock seeing Naruto appearing right behind them.

"H...how did you do that?!" Both women shouted

"Sorry that's classified." Naruto said flashing his foxxy grin that caused both women to blush.

"I came here as an escort for the officers who have been specially trained to pilot it," said Mu, looking back at Murrue and referring to the Strike. "Where can I find them?"

"The bombs detonated near the control booth," said Natarle. "Where the captain was welcoming them at that very moment. So they were also…"

"Yes, I see," said Mu. He then started walking up to Kira, the others following behind.

"What? What's the matter?" asked Kira. Lacus's grip on his hand tightened.

"So tell me," said Mu kindly. "You're a Coordinator?"

There was a somewhat shocked silence following Mu's words. Kira squared his shoulders.

"Yes," he said. A few of the Earth Forces soldiers gripped their rifles a little tighter, but Tolle and Naruto stepped in front of Kira, glaring at the soldiers.

"If you guys try to do anything to my friend. I'll kill you!" Naruto said with fearsome glare causing the soldiers to step back in fear as a crimson aura of killing intent surrounded the young man.

"N...Naruto.." Kira said shocked at his behavior, never before had he seen his friend sound so murderous before.

"It doesn't matter if he's a Natural or Coordinator, he's a human being!" Naruto said fiercely in defense of his friend.

Lower your rifles!"

Murrue stepped into the firing line and commands the soldiers who pause for a few seconds before doing as she asked. Natarle stepped in front of her with a confused expression.

"Lieutenant Ramius!" She addressed her superior, "please explain yourself." Murrue adopts a small smile and looks at Natarle.

"There's no puzzle, is there?" She asked rhetorically, "Heliopolis belongs to a neutral state, after all." She gave her a solemn expression.

"It's obvious that some coordinator would choose to live and avoid being involved in the war." She then turned towards Kira, "am I right?"

"No, you're right." Kira responded, "Especially with me being a first-generation coordinator."

"First-Generation?" Romero asked.

"Meaning that your parents are Naturals." Mu stated before scratching his head in embarrassment, "well, I apologize for causing a stir. I was just curious, is all." He says before turning towards Naruto. "And you?"

Naruto smirked as he lifted up his shirt slightly exposing several of the scars that covered his body. Kira and the others were shocked Mir covered her mouth with her hands looking horrified at the sight. "If I was would I have scares like this?" Naruto asked as shocked Mu.

(On board the Vesalius, Bridge.)

"I should thank you for bringing this to me, Miguel. If I didn't have this as proof then I would have become a laughing stock for allowing my CGUE to get damaged in a battle against one of the Earth Alliance's mobile suits." said Rau as he explained the situation to his team.

Athrun, on the other hand, was oblivious to this silent confrontation, lost in his thoughts. 'It couldn't have been... Kira...?' he thought in dismay.

"There is no way we can let mobile suits that powerful get away!" Rau announced. "If you can't capture them, then destroy them! Along with that new battleship of theirs!"

Capt. Ades stepped forward and started barking orders. "You heard the Commander! All hands, assume battlestations! Miguel, Olor and Matthew, prepare for launch! The Commander has authorized the use of Type-D Equipment!"

"Yes sir!" the three pilots said as they saluted.

After they had departed, Athrun immediately went up to the Vesalius' captain. "Capt. Ades! Please! Allow me sortie as well!" he requested, nearly pleaded.

"But you don't have a mobile suit to pilot," Le Creuset replied. "And besides, you've already completed the crucial mission of capturing one of the enemy's prototypes."

"Let this one go, Athrun Zala," Ades admonished. "Miguel, Olor, and Matthew are itching for action just as much as you are."

"... Yes, sir..." he replied, but his thoughts were still on his old friend.

'Kira...'

Aboard the Gamow, Pilot Ready Room

The engineering crews are hard at work attaching the fabled "D-Equipment" to the Ginns. One of the numerous weapons containers open to reveal the M66 "Canus" Short Ranged Guided Missile Launcher and M68 "Pardus" Short-range guided Three-Barrel Missile Launcher.

"Number Six Container!" One of the Engineers called out, "mount the D-Equipment onto the Ginn"

One of the Ginns moved forward, ready to receive this equipment.

"Operation commences at 01:00!" The announcer called over the intercom, "Matthew, proceed to standby position!"

Meanwhile, from the Locker Room, Nicol, Dearka, Yzak watched the GINN's through the observation window as the ZAFT Greens are preparing to sortie.

"D-Equipment, huh…" Dearka started to say, "Does Le Creuset plan to storm a fortress or something?"

"But what'll happen to Heliopolis?" Nicol asked his comrades with concern.

"Can't be helped, can it?" Dearka responded.

"It serves them right," Yzak stated, "calling themselves a neutral state."

Nicol only looked at Yzak for a few more seconds before turning to regard the Ginns, once again.

(Archangel)

Naruto was inside the cockpit of the Kurama sitting with is eyes close as he took the recent events that had unfolded. 'It seems like I can't keep living a life peace and security anymore.'

" **Yeah** **its about time!** " Kurama said

'Back off furball." Naruto said glaring at Kurama

"Oh come on Naruto! Its been centuries since we've been able to enjoy a battle." Kurama moaned as he complained while Naruto rolled his eyes, the young sage soon noticed Kira walking into the hanger looking up at the Earth Forces Mobile Suit.

'Kira has the potential to be a great warrior, but he's just to kind he lacks the will to kill. I've seen that look many times over the centuries young men and women forced into wars and made to take lives.' Naruto thought.

The young Coordinator was lost in his own thoughts about what he should do right now.

"Hey Kira." Naruto said looking down at his friend waving from the Kurama's Cockpit.

"Hey Naruto." Kira said with a smile as his friend jumped down to meet.

"What's wrong?" Naruto asked Kira looked away not wanting to talk about the conversion he had with the Captain.

"Let me guess they want you to plot the Strike again don't they." Naruto said Kira's silence more than answered his question."Say Kira..." Naruto asked as he turned to his own Gundam. "Do you've people that a precious to you?" Causing the boy look at him with a raised eyebrow.

"People who are precious to me?" Kira asked.

Naruto nodded. "Yes, when you have something or someone you truly care about that are irreplaceable. You fight with all your heart and soul to defend them. That's the reason I pilot my mobile suit, to protect all my precious and irreplaceable friends that's my reason to fight." Naruto said with a tone of utter conviction before turning to Kira with a serious expression he'd never seen in his friend before. "Fight so that you can protect your friends Kira." Naruto said before walking away to his room.

"Fight to protect my friends.." Kira repeated taking Naruto's words to heart.

(Onboard the Vesalius)

Olor and Matthew have just launched from the Nazca-Class with their D-Equipment attached. Meanwhile, Miguel was just getting ready to launch with his GINN that was equipped with the M69 "Barrus" Heavy Ion Cannon equipped and, rather strangely, has elected to take a Heavy Sword with him.

"Olor unit takeoff complete." The Flight Controller declared, "Miguel to the Catapult!"

"I'll get you this time!" Miguel muttered to himself as he rembered the humiliation dealt to him by the Kurama ,"Miguel Aiman, GINN, launching!" he yelled as his GINN shot out of the Hangar, detaching its power cable in the process as he hurried to catch up to his comrades its thrusters propelling itself towards Heliopolis.

"Alright! That's the last one! Close the hatch!" one of the mechanics announced over the comm system.

As he was about to hit the switch on the hatch, another mobile suit, this one brilliant red, stepped onto the catapult.

"Huh? This one's going out, too?"

Onboard the Aegis, Athrun was still deep in his thoughts.

'I have to find out... Was it really Kira in that mobile suit?'

Shaking his thoughts aside for the time being, Athrun hit the boosters and propelled the Aegis into space.

"Capt. Ades!" the ship's mobile suit controller shouted. "Athrun Zala has just launched in the captured mobile suit!"

"What?" Ades replied. "Call him back at once!"

"It's alright. Let him go," Rau said, countermanding Ades' orders.

"Commander?" Ades asked.

"Its data has already been extracted," Le Creuset replied. "Besides, aren't you curious to see what happens... when two Earth Alliance mobile suits clash?"

(Archangel)

The ship-wide alarm is roaring as Delida is alerted to the fact that they no longer have visual communication to surrounding area as evidenced by the static screen on his Display as well the large amount of Jamming Bars.

"Electrical Interference throughout the Colony!" He informed the bridge crew, "N-Jammer levels rising!"

"What?" Natarle asked as she turns her chair around to regard Delida. Mu let out a grunt of annoyance as he can easily assume what's causing this.

"It seems he has no intention of waiting until we get out of here!" Mu exclaimed with annoyance, "The bastard!"

"Do they intend to hit us again within the colony?" Natarle asked him.

"Easy for them" Mu stated playfully, "We can't fire, but they can fire as much as they want!"

(Archangel Mobile Suit Bridge.)

Naruto was walking over to board Kurama when he noticed Kira walking over to the Strike and smiled.

"I see you've made your choice eh Kira." Naruto said

Kira smiled and nodded "Yeah, you were right Naruto." Kira said. "If I'm gonna fight, I'm gonna do it to protect my friends.

"Good to here, now..Let's Kick Ass!" Naruto grinned as he and Kira ran over to they're respective Gundam's.

(Archangel Hanger)

The Archangel's engines roar into life as the White Ship takes off from the ground, kicking a large cloud of dust behind it from its launch. The crew have all manned their stations and Murrue has managed to make it back to the Bridge in time for launch.

"Our top priority is to escape Heliopolis." Murrue explained to the bridge crew, "be careful not to damage the Colony during battle!"

"That's impossible," Jackie muttered to himself, Natarle silently regards him."

The radar bursts into life as a contact appears on it, alerting the Bridge Crew.

"One heat source approaching!" Jackie called out, "The thermal pattern, it's a GINN!" He declared as a Ginn's blueprint screen appears as well as a video of the Ginn approaching, equipped with the Missile Launchers.

"What are they thinking?!" Mu exclaimed, "It has heavy bombing equipment used to take out bases! Are they planning to use that here?!"

Suddenly an explosion occurs as another hole is ripped in the side of the Colony as two more Ginns fly through the hole into Heliopolis

"A separate time is approaching from the Tannenbaun District." Jackie confirmed for them.

All of a sudden, a certain crimson Mobile Suit also appears through the tear which reveals itself on Jackie's Radar to which he lets out a gasp of surprise.

"One of them is X303, Aegis!" Mu, Natarle and Murrue all gasp at what they just heard.

"Launch the Strike and the Kurama." Natarle commanded

(Hanger)

"You ready Kira?" Naruto asked his friend

"Ready when you are." Kira said from within the Strike equipped with a sword pack.

"Then let's go!" Naruto said as he took off on the Kurama with Strike following behind it.

They're already sending it into actual battle?" Murrue asked with a disbelieving tone.

"Right now it's an enemy!" Mu stated, "do you want to be sunk by it?"

"Prepare to fire Korinthos!" Natarle ordered, "Direct Laser Designator at the GINNs!" Murrue turned to regard her.

"Projectile Weapons are useless against Phase Shift Armor!" She reminded Natarle, "Link laser to main cannons, fire at will!"

The Archangel's two "Gottfried MK.71" 225CM High Energy Beam Cannons rise from the front of the Archangel, extend their cannons, and take aim at the Mobile Suit Squad. Four large beams of Green Energy burst from the cannons and veer straight towards the enemies. Unfortunately, they all manage to dodge the oncoming attacks. Miguel's GINN then regards Athrun.

"Olor and Matthew, focus on the warship!" Miguel commanded his two fellow Greens, he then turns to Athrun, "Athrun! You came against orders. Now show us some more of that spirit and help me beat those two suits!"

As Miguel addressed Athrun, the Aegis focuses on the incoming Mobile Suits of the Strike and Kurama. Athrun regards it with a quiet expression before eventually responding to Miguel. "Sure."

"I'll deal with the other one." Miguel said eager to settle the score with the Orange and Black Gundam.

Naruto sensed something a saw the Orange Ginn from last time charging towards him, Naruto brought out its long sword and charged towards the Ginn who brandished its sword circling around one another.

"You! Your going down today!" Miguel shouted taking a swing at Naruto who blocked it with his sword before kicking it in the chest knocking him back.

"Damn this guys got some good moves!" Miguel shouted as The Kurama charged towards GINN dodged the sword barely and fires another blast at the Kurama hitting its mark and causing a large flash of light to occur.

"Did I get him?!" Miguel wonders with a hopeful smile. The smoke cleared from the Kurama to see it standing there without a scratch "NOT A SCRATCH! WHAT KINDA ARMOR IS THAT!" Miguel yelled in shock.

"Sorry that's a my little secret." Naruto said with a ,smirk as Miguel growled and continued to fire at Kurama who swiftly avoid the every shot fired.

Naruto soon noticed the two Ginns headed for the ship and grit his teeth. "Damn it they're going after the ship." Naruto notice that Kira was engaging the Aegis but the two mobile suits simply circled each other not even bothering to attack each other. 'Something's up with Kira and that Mobile Suit, it feels the same as me and Sasuke.' Naruto thought recalling his former best friend.

Naruto turned back to the Ginn he was facing "Sorry pal, I can't play along with you right now!" The Kurama dashed forward at Miguel's Ginn who continued to fire the orange gun the Kurama pulled reached out from behind and pulled out a beam shuriken and laucned it at Miguel who managed to evade it. Unfortunately, the beam shuriken flies like boomerang back around and slices the bottom part of the Ginn's right thrusters as well as its leg. "WHAT?!" He cried out. Naruto let out a loud shout as he kicked the Ginn down onto the hard ground of floor the Colony.

"Damn it! My machines completely useless now." Miguel groaned messing around with the machines controls before he quickly got out the mobile suit.

With that done Naruto turned his attention back to the two Ginns attack the Archangel. The Gundam pulled out its beam saber pushing on its thrusters as it charged at the two Ginns slicing one of them in halve before the second was hit by one of the Archangel's Gottfrieds, the powerful beams vaporizing the entire lower half of the mobile suit. But the beams continued on their path, hitting the central shaft of Heliopolis, and causing further damage.

'Damn it! At this rate...' Naruto said knowing that Heliopolis was on the brink of its destruction.

Just before the mobile suit exploded, it wildly fired off its two remaining missiles. The two out-of-control missiles hit the shaft. The shaft then broke into two, and with its central support gone, Heliopolis began to collapse.

Strike and Aegis

"Kira!" Athrun's voice called over the comm, "Kira Yamato!" Kira gasps as he recognized the voice easily.

"So it is you, isn't it, Kira?"

"Athrun? Athrun Zala?" Kira said in complete disbelief. "Why... why are you here?"

"You should talk, Kira!" Athrun countered. "What are you doing in that thing?"

Before Kira could even reply, the colony around them began collapsing. He looked around in horror, watching his home tear itself apart. And, just like that, the two friends were pulled apart by the vacuum in opposite directions.

Kira screamed as the G-forces his body was being subjected to grew too much for him to handle. He heard Athrun shout his name out over the comm, and then nothing but static.

(Onboard the Gamow)

The remaining pilots of the Le Creuset team watched as Heliopolis broke apart before their very eyes.

"Damn... how did Miguel and the others screw up so badly that the entire thing came apart?" Dearka asked no one in particular in frustration.

(Heliopolis Debris Field)

"Heliopolis… Destroyed?" Kira muttered to himself with disbelief as Natarle kept repeating her line over the communicator, hoping to hear some sign of confirmed existence from the pilot. "Why…?"

"Damn it!" Naruto shouted slamming his hand on the controls of his mobile suit shaking with rage as he looked at the now ruined colony floating around him.

(Archangel…)

The students of Heliopolis have just witnessed the devastation, all with their own visible forms of reaction to it.

Mirrialia and Tolle hold each other tightly at the sight of it and feel some sort of protection from the destruction that threatened to engulf the ship.

Sai can only look at what has occurred with upset while trying to comfort Serena as well.

Kuzzey is crouched on the ground whimpering, his hands clutching his head in terror.

Meanwhile, on the bridge of the Archangel, even the soldiers cannot help but be upset by the disturbing site in front of them. Mu drifts to the front of the bridge to get a better look at the devastation that is visible on the view-screen.

"Amazing how simple… how fragile it was…" Mu commented. Murrue clenches her fist in anger at the destruction. Her lamenting, however, was interrupted by the Ensign located in the CIC behind her, whose voice caused her to swivel her chair around to properly address it.

"X-105 Strike! X-105 Strike!" Natarle kept calling over the comm in desperation, "Kira Yamato! If you hear me, if you're okay, respond!"

Kira managed to snap out of his distressed state with a gasp as he activated the communicator to respond.

Naruto was brought out his grieving thoughts by the raven haired woman's shouted and flew over to Kira clutching the Gundam's shoulders. "Let's go Kira, what's done is done..." Naruto said solemnly

Kira nodded and flowed the Kurama he then noticed a light in the distance and moved in to examine it, the light revealed itself to be the beacon of a damaged Heliopolis lifeboat. "Archangel, I've found a damaged lifeboat. I'm bringing it in," he called over the radio.

What? Who gave you the authorization to do that?" Badgiruel asked, obviously not pleased.'

"I'm bringing it in." Kira replies not caring about the ensigns displeasure.

"You can't just bring in a civilian lifeboat without proper authorize-!"

"Ah shut up! We're bringing the life pod back and that's that!" Naruto shouted over his comm causing the crew to jump in fear.

Natarle's eyes widened as a small blush crept on her cheeks before softly coughing into her hand. "Um...well yes authorization granted."

"Thank you." Naruto said with smirk before turning to Kira. "Let's head back Kira." Naruto said t the younger man who nodded both Gundams heading back to the Archangel.

.

.

 **And that as they say is a rap, I hope you all liked this chapter, don't forget to leave reviews and comment on the story.**


End file.
